There won't be any problem if you delete the account that the apps are connected to - until it comes time to update them. the apps will keep working fine, but Play won't know that your phone has the apps installed. If they're free apps, no problem. If they're paid apps, you'll have to pay for them again.
(Assuming "I have two emails listed under google acct." means "I have 2 Google addresses listed in my phone". If you mean that there are 2 emails in your gmail account, each one is separate. You can delete one without affecting any other one.)